Text-mining and information-retrieval services for molecular biology

Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.     

Physiological Aspects of Melon (Cucumis melo L.) as a Function of Salinity

Journal of Plant Growth Regulation - This study evaluated the effect of saline water irrigation (4.5 dS m−1) on growth, gas exchange and mineral nutrient content in eight melon accessions and...     

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.     

Reactive phenotypes after acute and chronic NK-cell activation

Several phenotypic changes have been shown to occur after NK-cell stimulation, involving molecules that have been proved to regulate NK-cell migration into tissues and NK-cell activation and proliferation as well as target cell recognition and killing. Here, we review the reactive phenotypes observed in vivo after acute and chronic NK-cell activation.     

NMR determination of Electrophorus electricus acetylcholinesterase inhibition and reactivation by neutral oximes

Neurotoxic organophosphorus compounds (OPs), which are used as pesticides and chemical warfare agents lead to more than 700,000 intoxications worldwide every year. The main target of OPs is the inhibition of acetylcholinesterase (AChE), an enzyme necessary for the control of the neurotransmitter acetylcholine (ACh). The control of ACh function is performed by its hydrolysis with AChE, a process that can be completely interrupted by inhibition of the enzyme by phosphylation with OPs. Compounds used for reactivation of the phosphylated AChE are cationic oximes, which usually possess low membrane and hematoencephalic barrier permeation. Neutral oximes possess a better capacity for hematoencephalic barrier permeation.NMR spectroscopy is a very confident method for monitoring the inhibition and reactivation of enzymes, different from the Ellman test, which is the common method for evaluation of inhibition and reactivation of AChE. In this work ¹H NMR was used to test the effect of neutral oximes on inhibition of AChE and reactivation of AChE inhibited with ethyl-paraoxon. The results confirmed that NMR is a very efficient method for monitoring the action of AChE, showing that neutral oximes, which display a significant AChE inhibition activity, are potential drugs for Alzheimer disease. The NMR method showed that a neutral oxime, previously indicated by the Ellman test as better in vitro reactivator of AChE inhibited with paraoxon than pralidoxime (2-PAM), was much less efficient than 2-PAM, confirming that NMR is a better method than the Ellman test.     

Dilation of human atria: Increased diffusion restrictions for ADP,overexpression of hexokinase 2 and its coupling to oxidative phosphorylation in cardiomyocytes

Cardiac energy metabolism with emphasis on mitochondria was addressed in atrial tissue from patients with overload-induced atrial dilation. Structural remodeling of dilated (D) atria manifested as intracellular accumulation of fibrillar aggregates, lipofuscin, signs of myolysis and autophagy. Despite impaired complex I dependent respiration and increased diffusion restriction for ADP, no changes regarding adenylate and creatine kinase occurred. We observed 7-fold overexpression of HK2 gene in D atria with concomitant 2-fold greater activation of mitochondrial oxygen consumption by glucose, which might represent an adaption to increased energy requirements and impaired mitochondrial function by effectively joining glycolysis and oxidative phosphorylation.     

Work ability of health care shift workers: What matters?

This paper aims at identifying variables associated with inadequate work ability among nursing personnel at a public hospital, considering factors related to socio-demographic, lifestyles, working conditions, and health outcomes. A cross-sectional study was conducted in a university hospital in S?o Paulo, Brazil, as part of a larger research study on tolerance to 12 h night work. Nursing staff included registered nurses, nurse technicians, and nurse aides; in total, there were 996 healthcare workers (878 female; 118 male) at the time of the study. Some 696 workers (69.9%) of the population agreed to participate. Data collection (October 2004-July 2005) was based on a comprehensive questionnaire about living and working conditions (including incivility at work, work demands, work control, and support), mental and physical health symptoms (fatigue and sleep problems), and work ability. This report presents analyses of the adapted Brazilian version of the Work Ability Index (WAI) and associated variables. The study population worked one of the following shift schedules at this hospital: 12 h nights followed by 36 h off or 9 h or 6 h day (morning or afternoon) shifts. The mean age of the respondents was 34.9 (S.D.+/-10.4) years of age; 31.5% of the participants held two jobs. Statistical analyses using a hierarchical multiple logistic regression model were performed to evaluate the factors associated with inadequate (moderate and low scores) of the WAI. The significantly associated factors were socio-demographic (income responsibility, sole breadwinner, raising kids, age group), working conditions (thermal discomfort, organization of the workplace, and verbal abuse), and health outcomes (high body mass index, obesity, sleep problems, and fatigue). In spite of limitations of the study design, results indicate that the nursing profession is associated with stressful working conditions, contributing to inadequate WAI. This is in addition to bad living conditions and precarious work. Intervention measures, either at the workplace or at individual levels, are necessary to prevent a decrease in work ability, even in this quite young working population.